Monday, May 23, 2016
13:30 - 15:00

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13:30 - 13:45: / 304-305 COMPARISON OF ZOOPLANKTON SPECIES IDENTIFICATION USING ENVIRONMENTAL DNA AND MORPHOLOGICAL METHODS FOR APPLICATION IN LAKE MONITORING

5/23/2016  |   13:30 - 13:45   |  304-305

COMPARISON OF ZOOPLANKTON SPECIES IDENTIFICATION USING ENVIRONMENTAL DNA AND MORPHOLOGICAL METHODS FOR APPLICATION IN LAKE MONITORING The advancement of DNA barcoding has opened doors to efficient species identification at finer resolutions. It is however important to explore the feasibility of Environmental DNA (eDNA) methods for biological monitoring applications. This study explores two objectives: to determine whether eDNA barcoding of a composite water sample is as representative as a zooplankton haul, and to compare data output and efficiency between eDNA and morphological species identification. To test this, we sampled 4 lakes recovering from acidification and metals contamination in Sudbury, Ontario, Canada. At each lake, we obtained 3 replicate one-litre water samples from the entire water column for DNA barcoding, and 6 replicate zooplankton samples (vertical hauls), 3 for morphological identification and 3 for DNA barcoding. We determined the variability among replicates for each of the 3 sample types, differences between sequenced water samples and zooplanktons hauls, and assessed the similarity between morphological and eDNA identifications. The results of this study allow us to gauge whether eDNA methods provide an efficient and cost-effective alternative or compliment to morphological identifications and reveals the implications to lake biomonitoring programs.

Nicole-Marie Novodvorsky (Primary Presenter/Author), Laurentian University, nnovodvo@gmail.com;


Lynne Witty ( Co-Presenter/Co-Author), Laurentian University, lwitty@laurentian.ca;


Mehrdad Hajibabaei ( Co-Presenter/Co-Author), Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, ON, Canada, mhajibab@uoguelph.ca;


John L Bailey ( Co-Presenter/Co-Author), Ontario Ministry of the Environment and Climate Change, jbailey@laurentian.ca;


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13:45 - 14:00: / 304-305 BARCODING MICRO-ZOOPLANKTON WITHOUT CULTIVATION BY HIGH-THROUGHPUT PARALLEL SEQUENCING

5/23/2016  |   13:45 - 14:00   |  304-305

BARCODING MICRO-ZOOPLANKTON WITHOUT CULTIVATION BY HIGH-THROUGHPUT PARALLEL SEQUENCING The lack of a planktons DNA barcode library at the species level constrains the functional assessment of the plankton community by use of metagenomic data of bulk samples. This is due to both the fragility of planktonic organisms and their small body size at micro- or less scale, for which the conventional Sanger sequencing method is inefficient for barcode sequences capture of planktonic organisms. Using zooplankton as examples, here we describe a newly developed method to capture barcode sequences from hundreds of specimens simultaneously using Next-Generation Sequencing (NGS) platforms. Mitochondrial cytochrome c oxidase I (COI) fragment barcodes from 410 specimens were recovered with Personal Genome Machine (PGM). Contaminating sequences were detected in at least half of the specimens (52.4%) and across all species. In some species, the clustering of more than one operational taxonomic unit (OTU) was probably related to mitochondrial heteroplasmy. Although overvalued biodiversity couldn’t be avoided completely, our comparative analysis suggested that it could be reduced by setting 92% as the sequence similarity cutoff for clustering OTUs in zooplankton COI meta-barcoding.

Xiaowei Zhang (POC,Primary Presenter), Nanjing University, zhangxw@nju.edu.cn;


Jianghua Yang ( Co-Presenter/Co-Author), Nanjing University, yangjianghua1012@163.com;


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14:00 - 14:15: / 304-305 CONTRASTING BIODIVERSITY PATTERNS FROM WATER AND BENTHOS AS SOURCES OF ENVIRONMENTAL DNA SEQUENCES FOR AQUATIC BIOMONITORING

5/23/2016  |   14:00 - 14:15   |  304-305

CONTRASTING BIODIVERSITY PATTERNS FROM WATER AND BENTHOS AS SOURCES OF ENVIRONMENTAL DNA SEQUENCES FOR AQUATIC BIOMONITORING Advances in high-throughput sequencing (HTS) can yield sequence information from biota in environmental samples without separating organisms. A wide range of samples including water, soil, sediments, gut contents and trap sampling can provide sources of environmental DNA (eDNA), yet benthic samples remain the main source of biodiversity information for aquatic biomonitoring applications. Since water samples are simpler to obtain and process than benthic samples, we explored the suitability of DNA extracted from water as an alternative source for biodiversity information of bioindicator taxa. Here we compare benthic and water samples collected in parallel from the same wetland ponds as sources of DNA for biomonitoring. By comparing patterns of sequence data at Molecular Operational Taxonomic Units (MOTU) and multiple taxonomic levels including order, family, genus and species, we show marked differences between biodiversity obtained from eDNA in water samples as compared to eDNA extracted from benthic samples collected from boreal wetlands. Our results indicate that eDNA extracted from water samples provides a poor biodiversity signal when compared to eDNA extracted from benthic samples.

Donald Baird ( Co-Presenter/Co-Author), Environment and Climate Change Canada @ Canadian Rivers Institute, University of New Brunswick, Fredericton, NB, Canada, djbaird@unb.ca;


Mehrdad Hajibabaei (Primary Presenter/Author), Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, ON, Canada, mhajibab@uoguelph.ca;


Shadi Shokralla ( Co-Presenter/Co-Author), University of Guelph, shadi.shokralla@gmail.com;


Joel Gibson ( Co-Presenter/Co-Author), Royal British Columbia Museum, jfgibson@uoguelph.ca;


Ian King ( Co-Presenter/Co-Author), University of Guelph, ianwilliamking@gmail.com;


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14:15 - 14:30: / 304-305 SENSITIVITY AND ACCURACY OF HIGH-THROUGHPUT METABARCODING METHODS USED TO DESCRIBE AQUATIC COMMUNITIES FOR EARLY DETECTION OF INVASIVE FISH SPECIES

5/23/2016  |   14:15 - 14:30   |  304-305

SENSITIVITY AND ACCURACY OF HIGH-THROUGHPUT METABARCODING METHODS USED TO DESCRIBE AQUATIC COMMUNITIES FOR EARLY DETECTION OF INVASIVE FISH SPECIES For early detection biomonitoring of aquatic invasive species, sensitivity to rare individuals and accurate, high-resolution taxonomic classification are critical to minimize Type I and II detection errors. Given the great expense and effort associated with morphological identification of many aquatic organisms, high-throughput metabarcoding has gained recognition as an alternative means to describe biodiversity in aquatic communities. Our research uses complementary lab- and field- based experiments to investigate sensitivity and accuracy of metabarcoding methods commonly used to characterize sample composition (specifically, larval fish assemblages). Lab experiments demonstrate pyrosequencing of genetic marker CO1 (cytochrome c oxidase) facilitates detection of fish species with biomass percentages as low as 0.02-1% of total sample mass and results from parallel morphological and genetic analyses of field samples demonstrate metabarcoding can improve species richness estimates. Limits to detection, however, vary interspecifically and are influenced by CO1 amplification bias and data processing methods that skew sequence biodiversity estimates from corresponding constructed biodiversity and increase the rate of detection errors.

Chelsea Hatzenbuhler (Primary Presenter/Author), USEPA/NHEERL/MED,ORISE, Duluth, MN, hatzenbuhler.chelsea@epa.gov ;


Joel Hoffman ( Co-Presenter/Co-Author), USEPA/NHEERL/MED, Duluth, MN, hoffman.joel@epa.gov;


John R. Kelly ( Co-Presenter/Co-Author), USEPA, NHEERL/MED, Duluth, MN, jackrusselkelly@gmail.com;


Julie Lietz ( Co-Presenter/Co-Author), ORISE participant, USEPA, NHEERL/MED, Duluth, MN, lietz.julie@epa.gov;


John Martinson ( Co-Presenter/Co-Author), USEPA, NERL/EERD, Cincinnati, OH, martinson.john@epa.gov;


Sara Okum ( Co-Presenter/Co-Author), USEPA/NERL/SED,ORISE, Cincinnati, OH, okum.sara@epa.gov;


Greg Peterson ( Co-Presenter/Co-Author), USEPA, Peterson.Greg@epa.gov;


Erik Pilgrim ( Co-Presenter/Co-Author), USEPA/NERL/SED, Cincinnati, OH, pilgrim.erik@epa.gov;


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14:30 - 14:45: / 304-305 THE TRUTH IS OUT THERE: INTEGRATING DNA-BASED DATA INTO BIOASSESSMENTS IMPROVES OUR UNDERSTANDING OF SPECIES DISTRIBUTIONS AND SPECIES-HABITAT RELATIONSHIPS

5/23/2016  |   14:30 - 14:45   |  304-305

THE TRUTH IS OUT THERE: INTEGRATING DNA-BASED DATA INTO BIOASSESSMENTS IMPROVES OUR UNDERSTANDING OF SPECIES DISTRIBUTIONS AND SPECIES-HABITAT RELATIONSHIPS The integration of DNA-based identification methods into bioassessments could result in more accurate representations of species distributions and species-habitat relationships. DNA-based approaches may be particularly informative for tracking the distributions of rare and/or invasive species that can comprise a small proportion of samples or are difficult to identify morphologically. In 2012 and 2013, we used a combination of morphological and DNA-based methods (meta-barcoding) to identify fish eggs and larvae collected in the St. Louis River estuary area, Minnesota. We found a large proportion of cases where a lack of agreement occurred between species identified at a site using morphological versus DNA identification, prompting a discussion of how to best reconcile these differences. Choices made during sampling collection, DNA amplification/extraction, and bioinformatics processing influence the DNA-morphology match. The distribution of some species (including several invasives) and their relationships to habitat changed after DNA-data was incorporated. Results highlight how incorporating of DNA-data may get us closer to the “truth”, which has large ramifications in the search for rare species and when understanding the environmental drivers of species distributions is important for management.

Christy Meredith (POC,Primary Presenter), NRC Fellow, USEPA, MED,Duluth MN, Meredith.Christy@epa.gov;


Joel Hoffman ( Co-Presenter/Co-Author), USEPA/NHEERL/MED, Duluth, MN, hoffman.joel@epa.gov;


Anett Trebitz ( Co-Presenter/Co-Author), USEPA/NHEERL/MED,Duluth,MN, Trebitz.Anett@epa.gov;


Greg Peterson ( Co-Presenter/Co-Author), USEPA, Peterson.Greg@epa.gov;


Julie Lietz ( Co-Presenter/Co-Author), ORISE participant, USEPA, NHEERL/MED, Duluth, MN, lietz.julie@epa.gov;


Chelsea Hatzenbuhler ( Co-Presenter/Co-Author), USEPA/NHEERL/MED,ORISE, Duluth, MN, hatzenbuhler.chelsea@epa.gov ;


Erik Pilgrim ( Co-Presenter/Co-Author), USEPA/NERL/SED, Cincinnati, OH, pilgrim.erik@epa.gov;


Sara Okum ( Co-Presenter/Co-Author), USEPA/NERL/SED,ORISE, Cincinnati, OH, okum.sara@epa.gov;


John Martinson ( Co-Presenter/Co-Author), USEPA, NERL/EERD, Cincinnati, OH, martinson.john@epa.gov;


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